An Amethyst In The Rough
by MizuYamazai
Summary: A young orphaned girl with a mysterious past ends up discovering her true identity while falling in love. Warning - Gender -bending along with some lemons. Yami x Yugi. Atemu x Heba.
1. Prologue

**Mizu: Yay! My fanfic has been brought to life!**

**Bakura: Yeah, yeah. *rolls eyes***

**Mizu: I hope it goes well! XD**

**Ryou: Mizu Yamazai doesn't own anything related to Yu-Gi-Oh! or the Yu-Gi-Oh! series. The story and love for the characters are all she owns. **

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June 4th, 1996. It was the Celestial period of the Millennium world. Pharaoh Atemu had recently married the slave, Heba and had found out that his beloved was to have his child. It was on this day a miracle and a nightmare occurred. The day had began strangely. King Heba had awoken to a sharp pain that wouldn't cease. He immediately recognized it as him being in labor. Quickly, He woke up his husband. Atemu looked at Heba with confused dark crimson eyes. Heba winced in pain with pleading eyes. Atemu understood immediately.

"Isis! Seto!", He called. In a flash, two figures stood before him, a female with tan skin, dark hair and brown eyes and a male with lighter tan skin, brown hair and bright blue eyes.

"Yes, my King?", They asked, while bowing.

"It's Heba.", Atemu said, "He's gone into labor."

"I understand, my King. I shall help him.", Isis replied. Seto nodded and helped Atemu carry Heba as quick as they could to the healing chambers. Once there, Isis had shooed them away. Atemu and Seto stood outside, waiting. The other priests had joined them shortly.

"Alright Heba…Just relax. This will pay off in the end.", Isis said as she got him ready. Heba nodded, the pain too unbearable to speak. Outside, the wait was agonizing. Atemu had begun pacing, only stopping to listen in then go back to pacing. After 3 long and painful hours of pushing, breathing, crying, screaming, It was finally over.

Isis smiled softly at Heba, while holding a small wrapped bundle that cried quietly in her arms.

"Would you like to hold you new daughter, Heba?", She asked quietly. Heba nodded, as he reached out for her. Isis placed the crying bundle in his arms. Heba looked down at his newborn child and smiled. She had the same tri-colored hair like both of her parents only it fell down in ruffles. She didn't have any lightning streaks like her father Atemu but was precious just the same. She had soft, creamy milky white skin, unlike her parents tan skin. Her eyes were big and round with an amethyst color to them. However, one eye seemed to change to a slight crimson color, making her eyes seem like two different colors at once. Isis had already left the room quietly to inform the others. As soon as she opened the door, she heard a thud and a muffled Ow. Isis looked behind the door to see Atemu rubbing his nose slightly.

"Pharaoh Atemu, are you alright?", Isis asked.

"Yes, I'm fine.", He replied, smiling.

"Any news on the baby?", Seto asked.

At that, Isis smiled, "Yes. I'm very proud to say that you and Heba are the proud parents of a baby girl." Atemu smiled and without saying anything, went in to look at both his husband and child. Heba sat on the medical bed, holding close to him a bundle of blanket. Atemu walked over quietly.

"How are you feeling, Little star?", He asked lovingly.

Heba looked up, smiling, "I'm alright, Ate. Look. Isn't she beautiful?" Both looked down ant their newborn daughter, who had settled into Heba's arms quite well. She looked up once, her eyes curiously looking at the other stranger who looked like her mother.

"Yes.", Atemu agreed, smiling, "She's just as beautiful as you are."

"Well..", Heba replied, "What should we name her?" Atemu looked off to the side, thinking of a name fit for his little girl. He thought for a few minutes before looking down.

"How about Yugi?", Atemu asked him. Heba pondered over it. The name fit nicely.

"Alright.", Heba grinned, "Her name from now on will be Yugi Hikari Sennen." Little Yugi cooed at her new name. Both parents chuckled at that. As much as Atemu wanted to stay, he had to leave to inform the kingdom of their new princess. Isis had come back inside moments before, simply watching the new family as they shared smiles of love and affection.

Isis replied calmly, "I shall watch over the two for the night, Pharaoh." Atemu nodded, grateful to have a friend like Isis as the palace Healer. As he left, he gave Heba a quick kiss and Yugi a small kiss on her forehead. Outside the door, Seto looked at his cousin's beaming face.

"I take it that you're very happy now?", Seto asked.

"Yes.", Atemu replied, "Yes I am." He turned to the other priests.

"Before you offer your gifts, please wait one day. I wish for them to rest in peace.", Atemu said calmly. The priests nodded and followed the Pharaoh. He stepped out onto the balcony and looked down at the people of the square. After some formalities had been out of the way, Atemu proudly stated that today, his daughter, their new princess, had been born. Everyone in the kingdom cheered. Atemu smiled before heading about his day at the palace. Later on that evening, Isis went with Mahado, another trusted priest, down to an oracle named Ishizu. Ishizu was Isis's twin sister, and helped her in any way she could.

"Yes, sister?",Ishizu asked before Isis had even entered.

Isis smiled softly, "I wanted to ask you something. I felt a premonition earlier about the Pharaoh's new daughter. Could you explain it?" Mahado listened quietly with Isis as Ishizu began to speak.

"Yes. You were right. In a few days, their will be another attempt at the pharaoh's life however, the attempt will be made at his daughter instead." , Ishizu spoke calmly, "You both must make sure the assassin is to never find the princess, even if it means having to hide her away somewhere far from the palace." Isis looked at Mahado, who nodded quietly at Ishizu.

"I agree.", He replied.

Isis looked at Ishizu once more.

"Thank you for sharing that with us.", She replied quietly. The two then left to tell both the Pharaoh and King about what they had learned. As they walked through the palace, they came across, Atemu with Seto in the Healing chambers with Heba and Yugi. Isis's heart fell because if she told them this news, it would surely tear them apart. Mahado knew how Isis felt, but they had to tell them, to prevent the vision from happening.

"Ahem.", Mahado cleared his throat. Several pairs of eyes looked up at him and Isis.

"My Pharaoh, I went to visit my sister today.", Isis said calmly even though she felt like her voice was shaking.

"Ah,", Atemu replied, "How was it?"

"We learned some shocking news about Princess Yugi.", Isis replied.

Heba looked up, "what did Ishizu tell you?"

Before Isis could say anything, Mahado intervened saying, " She told us that Isis's premonition about the princess was right. In three days, My Pharaoh, an attempt on her life will be made in order to threaten yours." Everyone looked shocked. Heba began to hold his child protectively against him, while Atemu's rage was seething through his livid crimson eyes.

"However," Isis stated, "There is a way that we can keep this from happening but it involves having her leave the palace."

Atemu sighed. He had finally shared the love a family that he helped make and now this was the last day He'd ever feel that warmth. Heba looked into his daughter's eyes, feeling great sorrow well up from with in.

"We understand. Is there anyone that can care for her?", Atemu asked. Mahado looked at Isis.

Isis replied, "My sister Ishizu will watch over her. She'll be safest with her." Heba and Atemu looked at each other before looking at their daughter. She cooed quietly in their arms, her eyes suddenly sleepy. As soon as she fell asleep, Heba and Atemu placed two more kisses onto her tiny head along with a golden necklace of the eye of Horus with a ruby in it. Later that night, Princess Yugi had been handed over to Ishizu for protection. It had been three days later when they received the news. Ishizu had been killed during the night. And their princess had been lost forever. Or so they thought….

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**Mizu: alright, not bad for the prologue.**

**Seto: It's not as bad as most beginners, I must say**

**Yami: did you...did you just compliment her?**

**Mizu: Let's not jinx it! DX**

**Yugi: Review? Please? *cute puppy dog eyes***


	2. Warm Nights

**Mizu: Okay! More on Yugi and her friends in this chapter!**

**Yugi: I still don't get why I'm a girl**

**Mizu: Because you're sooo cute!**

**Yugi: *huffs* Mizu doesn't own anything.**

* * *

"Stop! Thief!" An unbiased crowd watched as someone came running past, clutching a loaf of bread in their arms. Several palace guards had been after the so-called thief. After running for hours, the thief looked around their surroundings before ducking into an alley way. An alley way with a dead end though, wasn't very smart for the thief.

"Gotcha Street Rat!", a guard shouted. The thief spun around, their cloak's hood falling down from the3 sudden movement. The guard gasped a bit. The thief wasn't a boy…but a girl! She had wide eyes of a dichromatic color, one a deep amethyst while the other was a bright crimson. Her long hair seemed spiked some and fell in ruffles. It was tri-colored, like that of the kings, Atemu and Heba. She too, had blond bangs, without lighting streaks along with jet black hair flowing underneath just meeting with amethyst tips. Her eyes narrowed a bit out of defiance. She clutched the loaf of bread to her chest.

"I earned it fair and square!", she glared.

"From what we were told, you stole it.", The guard sneered, "So now, you're gonna come with us." With that, he grabbed her wrist sharply, expecting it to be easy now he knew she was a little girl. Glaring, the thief kicked him squarely in the chest before scaling to the top of the alley's wall, running off. Grunting, the guard ordered the rest of his patrol men after her. She kept running until she noticed a small hut on the edge of the village. Smiling, she leapt down from the wall, running as fast as she could towards it. Outside at the hut were two young boys, one with platinum blonde hair and lavender eyes while the other had snowy white hair with deep chocolate eyes. They had been waiting since noon when their friend had left, promising to grab some food for them.

"Ryou! Look, she's coming!", the blond boy said excitedly. The white haired boy, known as Ryou, looked up in time to see his friend clutching a single loaf of bread, while running from what seemed to be palace guards.

"She's managed to reveal her identity as a thief hasn't she, Malik?", Ryou asked the blonde quietly before sighing. Malik simply nodded, sighing as well. As soon as their friend was inside, they shut the door, well prepared for the guards. Snickering, Malik watched with glee as the guards fell into a giant hole in the ground. Ryou had begun helping the other girl with putting the bread up.

"Sorry guys, I was only able to grab one loaf.", she said, her big eyes looking at the floor.

" It's alright, Yugi. At least you got some bread.", Ryou smiled, encouragingly. Yugi smiled before looking over at Malik. Malik grinned, holding up a peace sign signaling the guards had fallen for the trap hole. As soon as everyone settled down, Yugi made a big X on the day it was on their calendar. Tomorrow was a big day. It was signaled to be Yugi's birthday.

"Big day tomorrow, huh?" , Malik asked the young girl.

"Yes. Yugi'll be sixteen years old.", Ryou chuckled. Malik pretended to gasp in horror.

Malik pretended to pale, "No, not my little Yugi!"

Yugi laughed at the two._ They've been there for me since I can remember_, she thought. Yugi continued to laugh at them before turning to watch the sunset that had begun. Malik and Ryou smiled, joining her at her side. Yugi sighed, watching the sunset always made her feel happy and warm. She smiled as the first star soon appeared in the night sky. With that she quietly sang an old melody she remembered from long ago.

"Constant as the stars above

Always know that you are loved

And my love shining in you

Will help you make your dreams come true

Will help your dreams come true."

Ryou and Malik looked at each other with soft smiles. Every night, they heard her sing this as the first star came out of the sky. She had such an angelic voice matched with her innocence. Ryou looked at Malik with concern though. The guards had most likely escaped and were planning to tell the two kings about their new information on the tiny thief. Yugi continued watching the stars in bliss before the three heard a very loud rumbling noise coming from Yugi's stomach. Exchanging looks, they all laughed. Ryou went to the kitchen and made some porridge with toast. As all three sat down to eat, Yugi looked at the two.

"Should I start the prayer?", she asked. The two nodded. Yugi then put her hands together and prayed. " Dear gods, we thank you for this meal. May many of our days be blessed with happiness." As soon as the words were spoken, food started going down their throats. It was relatively quiet during any meal they had together. All three friends knew that it wasn't often they had peaceful evenings like this, so they took as much peaceful time as they could. By the end of the dinner, Malik chuckled when Yugi was having trouble staying awake. Ryou smiled and walked over to the young girl, helping her find her way towards her futon bed.

"Good night, Yugi.", Ryou whispered while tucking her in. Yugi simply nodded her goodnight with half-open eyes, rolling onto her side, immediately in a deep sleep. Ryou headed back to where Malik was. Malik seemed to be lost in thought.

"She's asleep", Ryou said while looking at his friend.

Malik sighed, "Tomorrow will be a bigger day than just celebrating her birthday."

Ryou nodded his agreement. Tomorrow was not only her birthday but the day that the young princess had gone missing. Every year, everyone was required to pay a visit to the palace with something the princess would have adored. It could be anything as well, so poor people wouldn't have to worry about it. Ryou sighed before turning to go to bed. Malik sighed before murmuring, "The secret's nearly out."

* * *

**Ryou: ...**

**Yugi: Ryou? what's wrong?**

**Yami: ah..aibou...you stole his line earlier.**

**Yugi: Eh?**

**Mizu: Ryou does the disclaimers. *huggles Ryou***

**Bakura: Hands off my hikari!**

**Mizu: -3- Make me!**

**Yami & Yugi: *sighs* Review, please.**


	3. Birthday Breakfast and Surprises

**Mizu: Another chapter and introducing...Dun dun duuuun! YAMI! XD**

**Yami: Yes, I finally enter**

**Jou: Let's get the story started already!**

**Ryou: Mizu doesn't own anything but the story.**

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Sun soon arose over the horizon near the small hut. Blinking, Yugi sat up, still slightly dazed with sleep. She went over to where Ryou and Malik normally were when sleeping only to find them not in bed. Yugi quickly ran out of the room only to bump into Malik.

"Well Lookie here. The birthday girl's up!", Malik chuckled. Ryou popped his head out of the kitchen and smiled before heading back, working on a surprise breakfast. Yugi looked at him, bewildered. She was so used to them being up after her. As she headed towards the kitchen, Malik stopped in front of her. She tried to go around him but he didn't let her.

"I'm hungry, Malik.", she whined, using her irresistible pouting face. Malik took a deep breath because even he needed some strength to turn her down.

Malik just grinned, "Sorry, Yugi. It's a surprise breakfast made by Ryou himself." Yugi smiled. Ryou was known by few to have a certain touch for culinary arts. Yugi always loved it when he would make a surprise meal.

Grinning, Yugi asked, "Should I grab something from the marketplace then?" Malik pretended to think before handing her a small list.

"Just grab some more of these and we'll be good to go.", He replied. Yugi glanced at it and nodded. Before she left though, She went down to the river near their small hut to bathe. Unknown to her, another had chosen that spot to bathe as well.

Morning had begun too early for Atemu and Heba. First after eating breakfast, they had to sit through a boring conference with boring people giving boring speeches. Then they had to wait until the prince from the Indian countries to visit. (( Atemu…)), Heba whined through the mind link. (Yes, little star?), Atemu asked. ((I'm booooooored…)), Heba replied. Atemu chuckled slightly. He was bored as well but today wasn't the day to just go back to bed. It was the day of remembrance of their little girl they lost sixteen years ago. (You'll live.), Atemu replied. Heba just huffed and looked the other way. Soon they heard a knock at the door.

"Enter.", Atemu's voice boomed throughout the throne room. A young man with two body guards next to him walked into the throne room. He had a sense of royal air around him but didn't seem the type to flaunt it at all. What was most intriguing was the fact he looked very similar to Pharaoh Atemu but with only pale skin. The young man then bowed before saying, "Greetings, Your highnesses. I am Prince Yami Mutou."

Heba was curious and asked, "What brings you here, Prince?"

Yami smiled sincerely before replying, " I learned that today was your country's annual festival for the lost princess. I merely came to express my condolences. I have a few gifts, I believe your daughter would have liked."

"I see." , Atemu replied, "Very well. We'll have a servant show you to your quarters immediately."

Yami bowed, "Thank you, your highnesses." He soon left, with intentions to look around the palace grounds.

As Yugi stepped into the cool Nile river, she looked if anyone was watching her. Realizing that no one was present, She slipped her pale body even further in. To any one else, it would have looked like she was drowning. And that's exactly what it looked like to a lad with dirty blonde hair and brown eyes. Concerned, he rushed over, grabbing one of her arms and pulling her up. She coughed and struggled against him.

"H-Hey! What's the big idea?!", Yugi sputtered while looking at the person who had grabbed her. The blonde realized that she wasn't wearing any clothing and quickly let go.

"Jeezus!", He cried out, "Were ya tryin to drown nude or something?!" Yugi turned and looked at the blonde. She was shocked and then embarrassed. A boy had seen her naked. A. BOY. She quickly got up out from the river, grabbing her clothing, pulling her dress over her head. She quickly grabbed her cloak and began to run. 'That…That pervert!', she thought while running. Back at the river, the blonde just shook his head in disbelief. After drying off, He walked back to his home and lover, which was the palace. His lover? None other than High Priest, Seto Kaiba. As he walked inside, a pair of arms wrapped around his waist. He smiled some.

"Hi Seto.", he said

"Where were you, Puppy?", Seto replied.

"Oh. Just out and about at the river side.", He replied. He hugged Seto back before letting go. Both would have continued much farther than a hug had Atemu and Heba not been there. Atemu rolled his eyes while Heba cleared his throat.

"Seto, Jou. Think you could keep your lust for each other inside your bedroom?", Atemu asked.

Jou shrugged, "He's the one who came onto me first." Heba shook his head. As the two lovers walked off, Heba turned to Atemu sighing. He chuckled.

"They're always like that, Heba.", Atemu replied.

Heba nodded, "I know." He smiled at his husband, who smiled back. Both rulers did their best to smile on this bitter day.

In Seto's room, Jou and Seto had just gotten out of a long five minute make out session. Jou leaned against Seto, a soft smile plastered onto his face.

"So, what made you want to go to the river?" Seto asked.

Jou chuckled. "Felt like taking a bath there. Saw something interesting though."

Seto looked at him, "What was it?" and with that Jou proceeded to tell him how he thought someone was drowning and lifted them out only to find a small young girl who had pale skin and had a strikingly similar appearance to Atemu and Heba. Seto listened but his eyes slowly widened in shock.

"What?", Jou asked, "What I say?"

Seto looked at his confused lover. "You just described Princess Yugi."

* * *

**Mizu: I love it when another chapter is uploaded.**

**Bakura: Then why do you take so long to do 'em?**

**Mizu: I have to find inspiration!**

**Marik: Laaaaaaaazzzzy!**

**Mizu: *glares, leaves***

**Ryou: *sighs* Review please. **


	4. Markets with Thieves

**Mizu: Yes! New chapter!**

**Atemu: Is it me, or did she just come back from a sugar high?**

**Yami: no she definitely did.**

**Mizu: Oh hush! I only had chocolate.**

**Ryou: Mizu doesn't own anything but the story.**

* * *

Jou just stared at what Seto had said.

"C-c'mon, Seto. Don't kid around with that…Princess Yugi has been missing since she was a b-baby…" he replied. But he knew that Seto wasn't joking. He was wearing the look that said I - am - not - kidding upon his usually stoic face. Jou sighed while sitting down. "Well I didn't know who she was. For all I know, She's long gone by now." Seto slipped an arm around him, pulling him close.

"Well, We'll need to let Atemu and Heba know soon. It may be foolish to hope after all these years but we need to take the risk." Jou simply nodded his head. Meanwhile, Yami had gotten bored with the palace and decided to travel out to the open market area. He went with a cloak to keep up his disguise since he hated having people kiss up to him all the time. He was walking along perfectly fine, gazing at the stands and items people had to sell, hearing all sorts of offers. It wasn't long before he heard a ruckus be made, and seeing several guards chasing a young child who had been clutching a stolen basket of goods. She had a cloak on, hiding her face. Yami tried to step out of the way but was unfortunately to late. The young thief plowed into Yami, causing both of them to trip, the thief falling on top of Yami. Their fall had manage to knock both their hoods off but the tiny thief managed to pull hers back up quickly. The guards had caught up with them.

"Thank you, Prince Yami. You managed to catch the thief." A lead guard said. Yami didn't pay any attention to him. All he could see where bright gem-like eyes, one of a rich Amethyst color while the other was that of Crimson with a hint of amethyst to it. 'So beautiful', he thought. The owner of the gemlike eyes quickly got off him before trying to make a dash for it again. Yami, however, wanted to learn about the little thief more, so he reached out, grabbing the edge of her cloak, pulling it down. It revealed long tri-colored hair much like his own only she didn't have lightening streaked bangs as he did. Her skin was pale and she struggled to get out of his reach. Something shiny around her neck caught her eye. It was a golden necklace of the eye of Horus with a ruby stone in it. The guards gasped before growling, yanking her away from Yami.

"You're arrested for stealing, you little thief." they snarled. She struggled as the guards and Yami led her back to the palace, where she was to be trialed. Ryou and Malik were back at the hut. Worry was consuming them.

"Where is she?", Malik asked. Ryou looked over at the market square, where Yugi had just been a few moments ago.

"Malik…She's been caught." He said softly. Malik groaned at this. He knew that someday she'd get caught but he never thought it would happen today. The two put on sandals, seeing as they would have to pay the market a visit, to help Yugi. They then locked their door and headed off, being sure to keep their cloaks up, to hide their faces. After wandering around the square, they noticed a group of guards with Yugi in tow, followed by a Prince whom looked strangely like the pharaoh but with pale skin. Malik nodded at Ryou, before jumping onto a guard's back. Ryou waited for the fuss to begin before dashing in and grabbing Yugi's arm.

"Hey!", the guard shouted in surprise. Several of the guards had to use brute strength to pry Malik off. Amidst the commotion, Prince Yami noticed someone grab the small thief away. Yami noticed that this person was pale like him, with soft white hair. He watched as the two darted off. Once Malik noticed Yugi was gone and safe, he let go of the guard and gave a smirk to the prince before running off. Prince Yami just shook his head in disbelief.

"My prince.", the lead guard said, "We should go after them. They must be in cohorts with the thief." Prince Yami sighed. "Very well. However, I shall be heading back to the palace." He stated this and began walking back towards the palace, a few guards accompanying him along the way.

Meanwhile, Yugi, Ryou, and Malik had managed to hide away in a small alley. Yugi had finished removing her cloak before turning to Malik and Ryou.

"Are both of you crazy?!", She yelled. The two quickly covered her mouth with their hands. Yugi glared at them.

Malik glared back at her. "Shut up or the guards'll hear us!" He whispered quickly. Yugi nodded, still glaring at them. They sighed softly before letting go. Ryou looked at Yugi.

"I'm sorry, Yugi. But we were worried about you.", He replied. Yugi sighed.

"I understand. Just don't do that again!", she hissed. Ryou and Malik nodded their heads.

Meanwhile, Prince Yami had been inside the palace for quite some time, alone in his guest room, thinking hard about the thief he had seen today in the market. As soon as he entered the guest room he was using, He was instantly soaked.

"Marik. Bakura. What's the meaning of this?", He asked highly un-amused. The two said came out from the closet, grinning psychotic and wild grins.

Bakura started to laugh. "We wanted some fun!"

"Yeah, we just got here and we're already bored out of our minds.", Marik added. Yami simply rolled his eyes. He suddenly wondered how he had managed to stay friends with these two for so long. It hadn't been a while before the two pranksters had noticed their friend's head occupied with other thoughts.

"Hey Yami. What's up?", Marik asked.

"Yeah, tell us.", Bakura added in.

"Well, I went out to look around their town square and I got pulled into assisting the local guards capture a little thief.", Yami replied.

"So wait, you're over thinking because of that?", Bakura rolled his eyes while shaking his head.

"I didn't finish, Idiot.", Yami replied back.

"Then finish it already.", grumbled Marik. Yami then proceeded to tell them about how he was simply walking around without trying to be seen but ended up getting nearly trampled by guards chasing a small, petite girl who they claimed was a thief, when she clearly looked 14 or younger. The two shook their heads.

"So, what are you gonna do now?", Bakura asked.

Yami sighed as he grabbed a nearby towel, drying himself off. "Hopefully, I'll find them again and ask them some questions. Who knows?"

Marik nodded. "In the mean time….Bakura! Let's see where the game room is!"

Bakura grinned. "You're on!" The two quickly left Yami alone, as their new mission was locate the game room and keep boredom at bay by, what else, video games.

* * *

**Mizu: And Bakura and Marik are in!**

**Bakura: Took ya long enough!**

**Marik: finally!**

**Atemu & Yami: I sense future problems with these two...**

**Ryou & Yugi: Review!**

**Malik: Or Marik and Bakura will hunt you down with creepy music.**


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